Table 2.

Lead genome-wide significant SNP for each validated locus from the regional meta-analyses of oral and pharyngeal cancers combined and analysis of each cancer separately^a and pharynx cancer combined, as well as OC^a and OPC^a separately.

Region	SNP	chr:posb	Gene	EA/OAc	Info (Rsq)d	AFe case/control	OR	P	P het
Oral and pharyngeal cancer
4q23	rs1229984	4:100239319	ADH1B	A/G	Geno	0.03/0.06	0.56	2.29x10–15	0.002
6p21.32	rs3828805	6:32636120	HLA-DQB1	C/T	0.88	0.75/0.72	1.28	3.35x10–13	0.007
10q26.13	rs201982221	10:126157446	LHPP	D/I	Geno	0.03/0.02	1.67	1.58x10–9	0.50
11p15.4	rs1453414	11:5829084	OR52N2/TRIM5	C/A	Geno	0.23/0.20	1.19	4.78x10–8	0.55
Oral cancer
2p23.3	rs6547741	2:27855924	GPN1	A/G	0.98	0.50/0.54	0.83	3.97x10–8	0.34
4q23	rs1229984	4:100239319	ADH1B	A/G	Geno	0.03/0.06	0.57	1.09x10–9	0.02
5p15.33	rs10462706	5:1343794	CLPTM1L	T/C	0.97	0.12/0.15	0.74	5.54x10–10	0.84
9p21.3	rs8181047	9:22064465	CDKN2B-AS1	A/G	Geno	0.29/0.24	1.24	3.80x10–9	0.37
9q34.12	rs928674	9:133952024	LAMC3	G/A	0.89	0.14/0.12	1.33	2.09x10–8	0.88
Oropharyngeal cancer
4q23	rs1229984	4:100239319	ADH1B	A/G	Geno	0.02/0.06	0.55	8.53x10–9	0.05
6p21.32	rs3828805	6:32636120	HLA-DQB1	C/T	0.88	0.75/0.72	1.37	2.21x10–12	0.07

^aOC=oral cancer, OPC=oropharyngeal cancer;

^bSNP position according to NCBI genome build 37 (Hg19);

^cEA=Effect allele; OA=other allele;

^dGeno=genotyped, SNP, INFO, R² is the average across imputation batches;

^eAF=allele frequency of the effect allele